ABA-responsive Element Research Articles

Transcription Factor ERF194 Modulates the Stress-Related Physiology to Enhance Drought Tolerance of Poplar.

Drought is one of the main environmental factors limiting plant growth and development. The AP2/ERF transcription factor (TF) ERF194 play key roles in poplar growth and drought-stress tolerance. However, the physiological mechanism remains to be explored. In this study, the ERF194-overexpression (OX), suppressed-expression (RNA interference, RNAi), and non-transgenic (WT) poplar clone 717 were used to study the physiology role of ERF194 transcription factor in poplar growth and drought tolerance. Morphological and physiological methods were used to systematically analyze the growth status, antioxidant enzyme activity, malondialdehyde (MDA), soluble sugars, starch, and non-structural carbohydrate (NSC) contents of poplar. Results showed that, compared with WT, OX plants had decrease in plant height, internode length, and leaf area and increased number of fine roots under drought stress. In addition, OX had higher water potential, activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD), contents of chlorophyll, soluble sugar, starch, and NSC, implying that ERF194 positively regulates drought tolerance in poplar. The growth status of RNAi was similar to those of WT, but the relative water content and CAT activity of RNAi were lower than those of WT under drought treatment. Based on the transcriptome data, functional annotation and expression pattern analysis of differentially expressed genes were performed and further confirmed by RT-qPCR analysis. Gene ontology (GO) enrichment and gene expression pattern analysis indicated that overexpression of ERF194 upregulated the expression of oxidoreductases and metabolism-related genes such as POD and SOD. Detection of cis-acting elements in the promoters suggested that ERF194 may bind to these genes through MeJA-responsive elements, ABA-responsive elements, or elements involved in defense and stress responses. The above results show that ERF194 improved tolerance to drought stress in poplar by regulating its growth and physiological factors. This study provides a new idea for the role of ERF194 transcription factor in plant growth and drought-stress response.

Synergistic effects of nitrogen metabolites on auxin regulating plant growth and development.

Nitrogen is one of the important nutrients required for plant growth and development. There is increasing evidences that almost all types of nitrogen metabolites affect, at least to some extent, auxin content and/or signaling in plants, which in turn affects seed germination, plant root elongation, gravitropism, leaf expansion and floral transition. This opinion focuses on the roles of nitrogen metabolites, , , tryptophan and NO and their synergistic effects with auxin on plant growth and development. Nitrate reductase (NR) converts nitrate into nitrite, and was roughly positive-correlated with the root auxin level, suggesting a crosstalk between nitrate signaling and auxin signaling. Abscisic Acid Responsive Element Binding Factor 3 (AFB3) and Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) are also the key enzymes involved in nitrogen metabolite-regulated auxin biosynthesis. Recent advances in the crosstalk among , , tryptophan and NO in regulation to NR, AFB3 and TAA1 are also summarized.

PDC1 is activated by ABF4 and inhibits seed germination by promoting ROS accumulation in Arabidopsis

Seed germination is tightly regulated by multiple endogenous signaling molecules and metabolites, such as abscisic acid (ABA), the products of fatty acid β-oxidation for energy production and reactive oxygen species (ROS). In Arabidopsis the expression of pyruvate decarboxylase 1 (PDC1), which is involved in fermentation metabolism, was strongly induced by ABA during seed germination, suggesting that PDC1 might regulate seed germination in response to ABA. To prove this hypothesis, we characterized the role of PDC1 in ABA-mediated inhibition of seed germination. The percentages of seed germination and cotyledon greening of PDC1-deficiency pdc1 mutants were higher, whereas those of PDC1-overexpression lines were lower, than those of wild-type (WT) plants in the presence of ABA. Chromatin immunoprecipitation and electrophoretic mobility shift assays indicated that the ABA-responsive element BINDING FACTOR 4 (ABF4) transcription factor could bind to the PDC1 promoter and activate gene expression. ABA-induction of PDC1 expression was impaired in abf4–1 mutants, and overexpression of ABF4 in pdc1–1 plants can partially rescue their ABA-insensitive phenotypes. In addition, ABA-induced ROS accumulation was impaired in pdc1–1 seedlings, whereas it was enhanced in PDC1-overexpression lines, as compared with WT plants. Furthermore, the levels of free fatty acids were lower in pdc1–1 mutants, but higher in the PDC1-overexpression lines, than WT plants. This is consistent with the altered expression of fatty acid β-oxidation-related genes in these plants. Taken together, our results indicated that ABF4 activates PDC1 expression, thereby promoting fatty acid β-oxidation and enhancing ROS accumulation, leading to inhibition of seed germination in Arabidopsis.

Characterization of a Stress-Enhanced Promoter from the Grass Halophyte, Spartina alterniflora L.

Stress-inducible promoters are vital for the desirable expression of genes, especially transcription factors, which could otherwise compromise growth and development when constitutively overexpressed in plants. Here, we report on the characterization of the promoter region of a stress-responsive gene SaAsr1 from monocot halophyte cordgrass (Spartina alterniflora). Several cis-acting elements, such as ABRE (ABA-responsive element), DRE-CRT (dehydration responsive-element/C-Repeat), LTRE (low temperature-responsive element), ERE (ethylene-responsive element), LRE (light-responsive element), etc. contributed at varying degrees to salt-, drought- and ABA-enhanced expression of gusA reporter gene in Arabidopsis thaliana under the full-length promoter, pAsr11875 and its deletion derivatives with an assortment of cis-regulatory motifs. The smallest promoter, pAsr1491, with three cis-acting elements (a CCAAT box-heat responsive, an LRE, and a copper responsive element) conferred drought-enhanced expression of gusA; pAsr1755 (with an ABRE and a DRE) presented the highest expression in ABA and drought; and pAsr1994 with seven ABREs and two DREs conferred optimal induction of gusA, especially under drought and ABA. Arabidopsis transgenics expressing a known abiotic stress-responsive gene, SaADF2 (actin depolymerization factor 2), under both pAsr11875 and p35S promoters outperformed the wild type (WT) with enhanced drought and salt tolerance contributed by higher relative water content and membrane stability with no significant difference between pAsr11875:SaADF2 or p35S:SaADF2 lines. However, pAsr11875:SaADF2 lines produced healthy plants with robust shoot systems under salt stress and control compared to slightly stunted growth of the p35S:SaADF2 plants. This reestablished the evidence that transgene expression under a stress-inducible promoter is a better strategy for the genetic manipulation of crops.

Genome-wide investigation and expression pattern of PHR family genes in cotton under low phosphorus stress.

Phosphorus starvation response (PHR) protein is an important transcription factor in phosphorus regulatory network, which plays a vital role in regulating the effective utilization of phosphorus. So far, the PHR genes have not been systematically investigated in cotton. In the present study, we have identified 22, 23, 41 and 42 PHR genes in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. Phylogenetic analysis showed that cotton PHR genes were classified into five distinct subfamilies. The gene structure, protein motifs and gene expression were further investigated. The PHR genes of G. hirsutum from the same subfamily had similar gene structures, all containing Myb_DNA-binding and Myb_CC_LHEQLE conserved domain. The structures of paralogous genes were considerably conserved in exons number and introns length. The cis-element prediction in their promoters showed that genes were not only regulated by light induction, but also were related to auxin, MeJA, abscisic acid-responsive elements, of which might be regulated by miRNA. The expression analysis showed that the GhPHR genes were differentially expressed in different tissues under various stresses. Furthermore, GhPHR6, GhPHR11, GhPHR18 and GhPHR38 were significantly changed under low phosphorus stress. The results of this study provide a basis for further cloning and functional verification of genes related to regulatory network of low phosphorus tolerance in cotton.

Cloning and function analysis of DlWRKY9 gene in longan (Dimocarpus longan)

WRKY is one of the largest plant transcription factors (TFs) which is widely involved in plant growth, development, and responses to stresses. In the present study, a WRKY TF DlWRKY9 was cloned from longan (Dimocarpus longan). The coding sequence (CDS) of DlWRKY9 is 762 bp in length and encodes 253 amino acids. It has a typical WRKY domain and zinc finger structure which belongs to type IIa WRKY protein. The molecular weight of DlWRKY9 protein was 30.27kda and the theoretical isoelectric point (PI) was 5.24. It is an unstable hydrophilic protein. The secondary structure of DlWRKY9 protein consists of helical structure (17.39%), extended chain (8.70%) and other structures (turn and random coil) (73.91%). The amino acid sequence of DlWRKY9 protein had the highest similarity with DlWRKY9 (xp_006450293.1) of citrus Clementina. DlWRKY9 gene promoter elements contain light, abscisic acid, gibberellin, jasmonic acid and other response elements. The results of qRT-PCR showed that the relative expression level of DlWRKY9 gene in pericarp was higher, followed by young fruits and floral organs. Meanwhile, DlWRKY9 gene specifically down-regulated in the early stage of flower induction in ‘Sijimi’ (SJ) longan. The results of transient expression of Arabidopsis protoplasts showed that the fluorescence signal was mainly concentrated in the nucleus. Moreover, overexpression of DlWRKY9 in Arabidopsis promoted early flowering. These results provide useful information for revealing the biological roles of DlWRKY9 in longan and increase our understanding of the WRKY family in fruit trees.

Genome-Wide Characterization and Expression Profiling of HD-Zip Genes in ABA-Mediated Processes in Fragaria vesca.

Members of homeodomain-leucine zipper (HD-Zip) transcription factors can play their roles by modulating abscisic acid (ABA) signaling in Arabidopsis. So far, our knowledge of the functions of HD-Zips in woodland strawberries (Fragaria vesca), a model plant for studying ABA-mediated fruit ripening, is limited. Here, we identified a total of 31 HD-Zip genes (FveHDZ1-31) in F. vesca, and classified them into four subfamilies (I to IV). Promoter analyses show that the ABA-responsive element, ABRE, is prevalent in the promoters of subfamily I and II FveHDZs. RT-qPCR results demonstrate that 10 of the 14 investigated FveHDZs were consistently >1.5-fold up-regulated or down-regulated in expression in response to exogenous ABA, dehydration, and ABA-induced senescence in leaves. Five of the six consistently up-regulated genes are from subfamily I and II. Thereinto, FveHDZ4, and 20 also exhibited significantly enhanced expression along with increased ABA content during fruit ripening. In yeast one-hybrid assays, FveHDZ4 proteins could bind the promoter of an ABA signaling gene FvePP2C6. Collectively, our results strongly support that the FveHDZs, particularly those from subfamilies I and II, are involved in the ABA-mediated processes in F. vesca, providing a basis for further functional characterization of the HD-Zips in strawberry and other plants.

Genome-wide identification and characterization of NHL gene family in response to alkaline stress, ABA and MEJA treatments in wild soybean (Glycine soja).

NDR1/HIN1-like (NHL) family genes are known to be involved in pathogen induced plant responses to biotic stress. Even though the NHL family genes have been identified and characterized in plant defense responses in some plants, the roles of these genes associated with the plant abiotic stress tolerance in wild soybean is not fully established yet, especially in response to alkaline stress. We identified the potential NHL family genes by using the Hidden Markov model and wild soybean genome. The maximum-likelihood phylogenetic tree and conserved motifs were generated by using the MEME online server and MEGA 7.0 software, respectively. Furthermore, the syntenic analysis was generated with Circos-0.69. Then we used the PlantCARE online software to predict and analyze the regulatory cis-acting elements in promoter regions. Hierarchical clustering trees was generated using TM4: MeV4.9 software. Additionally, the expression levels of NHL family genes under alkaline stress, ABA and MEJA treatment were identified by qRT-PCR. In this study, we identified 59 potential NHL family genes in wild soybean. We identified that wild soybean NHL family genes could be mainly classified into five groups as well as exist with conserved motifs. Syntenic analysis of NHL family genes revealed genes location on 18 chromosomes and presence of 65 pairs of duplication genes. Moreover, NHL family genes consisted of a variety of putative hormone-related and abiotic stress responsive elements, where numbers of methyl jasmonate (MeJA) and abscisic acid (ABA) responsive elements were significantly larger than other elements. We confirmed the regulatory roles of NHL family genes in response to alkaline stress, ABA and MEJA treatment. In conclusion, we identified and provided valuable information on the wild soybean NHL family genes, and established a foundation to further explore the potential roles of NHL family genes in crosstalk with MeJA or ABA signal transduction mechanisms under alkaline stress.

Genome-Wide Analysis of AP2/ERF Gene Superfamily in Ramie (Boehmeria nivea L.) Revealed Their Synergistic Roles in Regulating Abiotic Stress Resistance and Ramet Development

AP2/ERF transcription factors (TFs) are one of the largest superfamilies in plants, and play vital roles in growth and response to biotic/abiotic stresses. Although the AP2/ERF family has been extensively characterized in many species, very little is known about this family in ramie (Boehmeria nivea L.). In this study, 138 AP2/ERF TFs were identified from the ramie genome and were grouped into five subfamilies, including the AP2 (19), RAV (5), Soloist (1), ERF (77), and DREB (36). Unique motifs were found in the DREB/ERF subfamily members, implying significance to the AP2/ERF TF functions in these evolutionary branches. Segmental duplication events were found to play predominant roles in the BnAP2/ERF TF family expansion. Light-, stress-, and phytohormone-responsive elements were identified in the promoter region of BnAP2/ERF genes, with abscisic acid response elements (ABRE), methyl jasmonate response elements, and the dehydration response element (DRE) being dominant. The integrated transcriptome and quantitative real-time PCR (qPCR) revealed 12 key BnAP2/ERF genes positively responding to waterlogging. Five of the genes are also involved in ramet development, with two (BnERF-30 and BnERF-32) further showing multifunctional roles. The protein interaction prediction analysis further verified their crosstalk mechanism in coordinating waterlogging resistance and ramet development. Our study provides new insights into the presence of AP2/ERF TFs in ramie, and provides candidate AP2/ERF TFs for further studies on breeding varieties with coupling between water stress tolerance and high yield.

Comprehensive in silico analysis of Phospholipase D gene family in economically important orchids

• A total of 25 putative PLD proteins from the genomes of Phalaenopsis equestris (7) , Dendrobium catenatum (9) and Apostasia shenzhenica (9) were identified. • These proteins are comprised of two HKD domains and two additional domains; C2 and PXPH domains at N-terminal region. • The multiple sequence alignment, domain and motifs analysis revealed their conserved nature and homology structure simulation and Ramachadran plot analysis revealed the abundance of beta sheets in tertiary structures. • The presence of Root-specific element, DOF proteins binding domain, scaffold or matrix attachment region, pollen-specific, dehydration-responsive, light-responsive, gibberellin-responsive, ABA-responsive elements and Meja-responsive upstream cis- regulatory promoter elements indicated their role in various physiological processes. Phospholipase D (PLD) plays a fundamental role in various aspects of plant growth, development and stress responses. In present study, 25 putative PLD proteins from the genomes of Phalaenopsis equestris (7) , Dendrobium catenatum (9) and Apostasia shenzhenica (9) were identified on the basis of presence of two HKD domains and two additional domains; C2 and PXPH domains at N-terminal region. These proteins were clustered into five sub-groups (α, β, δ, ζ and φ) along with their orthologs in Arabidopsis thaliana and Oryza sativa upon phylogenetic analysis. Gene characterization divulged that most of the PePLD, DcPLD and AsPLD genes within the same sub-group exhibited similar exon-intron organization and highly conserved motifs. RNA-seq based spatio-temporal studies indicated differential expression in various vegetative and reproductive tissues. PePLDα 1 , DcPLDα 1 and AsPLDα 1 were showing significant expression in all the tissues, while for other genes the expression was limited either in vegetative or reproductive tissues. Homology structure simulation revealed the abundance of random coils in secondary structures and beta sheets in tertiary structures. The presence of specific upstream cis- regulatory promoter elements emphasized the role of PLD s in various physiological processes. This report is the first genome-wide characterization of the PLD gene family in orchids and shall provide new insight into the functional characterization of these genes.

Genome-wide characterization of NAC transcription factors in Camellia sinensis and the involvement of CsNAC28 in drought tolerance.

The NAM, ATAF1/2, and CUC2 (NAC) transcription factors, which are members of a plant-specific gene family, play critical roles during the growth and development of plants and in their adaption to environmental stress. Few NAC transcription factors have been functionally characterized in tea plants (Camellia sinensis). Based on the analysis of the gene structure, motif pattern, and evolutionary relationship, we identified 104 NAC genes in C. sinensis. Among them, CsNAC28 is constitutively expressed in all organs, and most significantly, exhibiting remarkable responsiveness to abscisic acid (ABA) treatment and drought stress. ABA is a primary stress-related hormone. Recently, ABA-responsive element binding factor 2 (CsABF2) was identified in the ABA pathway of C. sinensis. However, the involvement of the CsABF2-mediated ABA pathway in regulating CsNACs was not known. Herein, a series of biochemical and genetic approaches supported the fact that CsNAC28 could potentially act as a transcription factor in the downstream of CsABF2. Furthermore, we investigated the function of CsNAC28 in the adapting of a plant to drought stress. The results showed that overexpression of CsNAC28 in Arabidopsis conferred hypersensitivity to ABA treatment and decreased the accumulation of reactive oxygen species (ROS), resulting in improved dehydration tolerance. Under conditions of drought, the expression levels of ABA pathway-related genes and drought stress‒inducible genes were greater in CsNAC28 overexpression lines than in the wild type. Our study's comprehensive characterization of NAC genes in C. sinensis could serve as a foundation for exploring the molecular mechanism of CsNAC-mediated drought responsiveness.

SnRK2.4-mediated phosphorylation of ABF2 regulates ARGININE DECARBOXYLASE expression and putrescine accumulation under drought stress.

Arginine decarboxylase (ADC)-mediated putrescine (Put) biosynthesis plays an important role in plant abiotic stress response. SNF1-related protein kinases 2s (SnRK2s) and abscisic acid (ABA)-response element (ABRE)-binding factors (ABFs), are core components of the ABA signaling pathway involved in drought stress response. We previously reported that ADC of Poncirus trifoliata (PtrADC) functions in drought tolerance. However, whether and how SnRK2 and ABF regulate PtrADC to modulate putrescine accumulation under drought stress remains largely unclear. Herein, we employed a set of physiological, biochemical, and molecular approaches to reveal that a protein complex composed of PtrSnRK2.4 and PtrABF2 modulates putrescine biosynthesis and drought tolerance by directly regulating PtrADC. PtrABF2 was upregulated by dehydration in an ABA-dependent manner. PtrABF2 activated PtrADC expression by directly and specifically binding to the ABRE core sequence within its promoter and positively regulated drought tolerance via modulating putrescine accumulation. PtrSnRK2.4 interacts with and phosphorylates PtrABF2 at Ser93. PtrSnRK2.4-mediated PtrABF2 phosphorylation is essential for the transcriptional regulation of PtrADC. Besides, PtrSnRK2.4 was shown to play a positive role in drought tolerance by facilitating putrescine synthesis. Taken together, this study sheds new light on the regulatory module SnRK2.4-ABF2-ADC responsible for fine-tuning putrescine accumulation under drought stress, which advances our understanding on transcriptional regulation of putrescine synthesis.

TaERF87 and TaAKS1 synergistically regulate TaP5CS1/TaP5CR1-mediated proline biosynthesis to enhance drought tolerance in wheat.

Drought stress limits wheat production and threatens food security world-wide. While ethylene-responsive factors (ERFs) are known to regulate plant response to drought stress, the regulatory mechanisms responsible for a tolerant phenotype remain unclear. Here, we describe the positive regulatory role of TaERF87 in mediating wheat tolerance to drought stress. TaERF87 overexpression (OE) enhances drought tolerance, while silencing leads to drought sensitivity in wheat. RNA sequencing with biochemical assays revealed that TaERF87 activates the expression of the proline biosynthesis genes TaP5CS1 and TaP5CR1 via direct binding to GCC-box elements. Furthermore, proline accumulates to higher levels in TaERF87- and TaP5CS1-OE lines than that in wild-type plants under well-watered and drought stress conditions concomitantly with enhanced drought tolerance in these transgenic lines. Moreover, the interaction between TaERF87 and the bHLH transcription factor TaAKS1 synergistically enhances TaP5CS1 and TaP5CR1 transcriptional activation. TaAKS1 OE also increases wheat drought tolerance by promoting proline accumulation. Additionally, our findings verified that TaERF87 and TaAKS1 are targets of abscisic acid-responsive element binding factor 2 (TaABF2). Together, our study elucidates the mechanisms underlying a positive response to drought stress mediated by the TaABF2-TaERF87/TaAKS1-TaP5CS1/TaP5CR1 module, and identifies candidate genes for the development of elite drought-tolerant wheat varieties.

Genome-Wide Identification and Expression Analysis of the NAC Gene Family in Kandelia obovata, a Typical Mangrove Plant.

The NAC (NAM, ATAF1/2, and CUC2) gene family, one of the largest transcription factor families in plants, acts as positive or negative regulators in plant response and adaption to various environmental stresses, including cold stress. Multiple reports on the functional characterization of NAC genes in Arabidopsis thaliana and other plants are available. However, the function of the NAC genes in the typical woody mangrove (Kandelia obovata) remains poorly understood. Here, a comprehensive analysis of NAC genes in K. obovata was performed with a pluri-disciplinary approach including bioinformatic and molecular analyses. We retrieved a contracted NAC family with 68 genes from the K. obovata genome, which were unevenly distributed in the chromosomes and classified into ten classes. These KoNAC genes were differentially and preferentially expressed in different organs, among which, twelve up-regulated and one down-regulated KoNAC genes were identified. Several stress-related cis-regulatory elements, such as LTR (low-temperature response), STRE (stress response element), ABRE (abscisic acid response element), and WUN (wound-responsive element), were identified in the promoter regions of these 13 KoNAC genes. The expression patterns of five selected KoNAC genes (KoNAC6, KoNAC15, KoNAC20, KoNAC38, and KoNAC51) were confirmed by qRT-PCR under cold treatment. These results strongly implied the putative important roles of KoNAC genes in response to chilling and other stresses. Collectively, our findings provide valuable information for further investigations on the function of KoNAC genes.

OSCA Genes in Liriodendron chinense: Characterization, Evolution and Response to Abiotic Stress

The hyperosmolality-gated calcium-permeable channels (OSCA) play an imperative role in the plant response to environmental stresses. Moreover, their characteristics in the ornamental woody plant Liriodendron chinense, widely dispersed in the southern region of China, is yet to be elucidated. In the present study, 399 OSCA proteins were identified from 31 plant genomes, and comparative phylogenetic analysis revealed that LchiOSCAs gene family is closely related to the Magnolia Cinnamomum kanehirae OSCAs. In L. chinense, 11 LchiOSCA genes were identified and distributed across eight chromosomes. Additionally, phylogenetic analysis of LchiOSCAs exhibited a classification into four subfamilies based on the tree arrangement, similarity in the gene structures, and conserved motif numbers and order. Gene duplication investigations were biased towards the tandem duplication events, accounting for 36% (4/11) of the LchiOSCA gene family. The interspecies collinearity analysis revealed a closer relationship between the L. chinense OSCAs and the P. trichocarpa OSCAs. Analysis in promoter regions of the LchiOSCAs showed the presence of multiple phytohormones and stress responsive elements. Specifically, the ABA-responsive elements had the greatest representation. 3D protein structures of the modeled L. chinense OSCAs exhibited a high homology with the template structures, providing a better understanding of LchiOSCAs’ functionality at the proteome level. The expression pattern analysis of LchiOSCAs based on the transcriptome data and qRT-PCR in L. chinense leaves showed differential responses to drought, cold, and heat stress at varying degrees. Specifically, LchiOSCA2 and LchiOSCA4 were highly expressed under the three abiotic stresses. This research will provide valuable resources and further the understanding of plant OSCA genes in L. chinense for agronomic breeding and bio-engineering purposes.

Identification and Comparative Analysis of the Rosaceae RCI2 Gene Family and Characterization of the Cold Stress Response in Prunus mume

Rare cold inducible 2 (RCI2) proteins are a group of low molecular weight proteins that widely exist in various tissues of plants and play crucial roles in plant growth and development and abiotic stress responses. Genome-wide identification and analysis of RCI2 have not been documented in Rosaceae plants. Therefore, we identified 23 RCI2 genes from seven Rosaceae plants, which were classified into three subfamilies. The RoRCI2 protein encodes a highly conserved domain of Pmp3. Three homologous PmRCI2s genes from Prunus mume were cloned and named PmRCI2-1, PmRCI2-2, and PmRCI2-3. The results of subcellular localization prediction showed that three PmRCI2s localized to membrane structures, and the abscisic acid response element were found to have the largest number in the promoter sequences of PmRCI2s. The results of quantitative real-time PCR (qRT-PCR) showed that PmRCI2-3 was significantly induced by low temperature and highly expressed in stems and buds during the endodormancy stage. Our study improves the understanding of the RCI2 family of Rosaceae plants regarding the cold responses and provides a theoretical basis for the cold-resistant breeding of P. mume.

Genome-Wide Identification and Expression Analysis of Senescence-Associated Genes in Grapevine (Vitis vinifera L.) Reveal Their Potential Functions in Leaf Senescence Order.

Natural leaf senescence is an acclimation strategy that enables plants to reallocate nutrients. In the present study, interestingly, we found that the basal mature leaves of grapevine primary shoots (P) exhibited the earliest senescence, followed by the apical young leaves of secondary shoots (ST), and then the basal mature leaves of secondary shoots (S). The Chl level decreased with the extent of leaf senescence. According to the genome-wide identification and expression analysis, sixteen senescence-associated genes (SAGs) involved in Chl breakdown were identified in the grapevine genome. Their expression patterns showed that the transcript changes in VvSGR, VvPPH2, and VvFtsH6-2 corresponded to the changes in Chl content among P, S, and ST. The changes in the transcription of VvNYC1, VvSGR, VvPAO1, VvPAO2, VvPAO4, VvPPH1, VvPPH3, and VvFtsH6-1 only contributed to low Chl levels in P. The cis-element analysis indicated that these SAGs possessed several light- and hormone-responsive elements in their promoters. Among them, ABA-responsive elements were found in twelve of the sixteen promoters of SAGs. Correspondingly, ABA-signaling components presented various changes in transcription among P, S, and ST. The transcription changes in VvbZIP45 and VvSnRK2.1 were similar to those in VvSGR, VvPPH2, and VvFtsH6-2. The other nine ABA-signaling components, which included VvRCAR2, VvRCAR4, VvRCAR6, VvRCAR7, VvRCAR2, VvPP2C4, VvPP2C9, VvbZIP25, and VvSnRK2.3, were highly expressed in P but there was no difference between S and ST, with similar expression patterns for VvNYC1, VvSGR, VvPAO1, VvPAO2, VvPAO4, VvPPH1, VvPPH3, and VvFtsH6-1. These results suggested that the senescence of P and ST could be regulated by different members of Chl breakdown-related SAGs and ABA-signaling components. These findings provide us with important candidate genes to further study the regulation mechanism of leaf senescence order in grapevine.

Overexpression of ONAC054 Improves Drought Stress Tolerance and Grain Yield in Rice

Drought stress negatively affects plant growth and development, thus reducing plant productivity. Therefore, understanding the molecular mechanisms underlying drought stress responses is essential for crop improvement. The plant-specific NAM/ATAF1,2/CUC2 (NAC) transcription factors play important roles in the drought stress response. Here, we show that rice (Oryza sativa) ONAC054, a membrane-bound NAC transcription factor, is involved in the drought stress response. We found that onac054 mutants were sensitive, whereas ONAC054-overexpressing (ONAC054-OX) plants were tolerant to drought stress. Under drought stress conditions, several genes associated with abscisic acid (ABA) synthesis and signaling were downregulated in onac054 mutants but upregulated in ONAC054-OX plants. Among these genes, the TRANSCRIPTION FACTOR RESPONSIBLE FOR ABA REGULATION 1 (TRAB1), which encodes an ABA-inducible bZIP transcription factor, was directly activated by ONAC054. On the other hand, the expression of ONAC054 was directly activated by several ABA-responsive elements (ABRE)-binding factors (ABFs) in an ABA-dependent manner, indicating that ONAC054 acts as an enhancer of ABA-induced drought stress tolerance. Additionally, the overexpression of ONAC054 in rice greatly improved grain yield under drought stress conditions, indicating that the overexpression of ONAC054 could facilitate the improvement of drought stress tolerance in rice and other crops.

Binding of the transcription factor MYC2-like to the ABRE of the OsCYP2 promoter enhances salt tolerance in Oryza sativa.

Cyclophilins, a type of peptidyl-prolyl cis-trans isomerase, function as important molecular chaperones in a series of biological processes. However, the expression pattern and signal transduction pathway of cyclophilins are still unclear. Here, we showed that the promoter of OsCYP2 could function as a tissue-specific promoter by GUS staining. Moreover, we found that the promoter sequence contained not only core elements but also inducible elements. Then, the ABA-responsive element was used for cDNA library screening, and the transcription factor MYC2-like was identified by a yeast one-hybrid assay and confirmed through an electrophoretic mobility shift assay. Furthermore, the relative expression showed that MYC2-like was induced by abscisic acid. In addition, MYC2-like overexpression enhanced salt tolerance in transformants and partially restored the cyp2-RNAi line. In summary, we explored a novel transcriptional signal mediated by MYC2-like, a potential regulator of salt stress-related physiological processes in rice.

The IbPYL8-IbbHLH66-IbbHLH118 complex mediates the abscisic acid-dependent drought response in sweet potato.

Drought limits crop development and yields. bHLH (basic helix-loop-helix) transcription factors play critical roles in regulating the drought response in many plants, but their roles in this process in sweet potato are unknown. Here, we report that two bHLH proteins, IbbHLH118 and IbbHLH66, play opposite roles in the ABA-mediated drought response in sweet potato. ABA treatment repressed IbbHLH118 expression but induced IbbHLH66 expression in the drought-tolerant sweet potato line Xushu55-2. Overexpressing IbbHLH118 reduced drought tolerance, whereas overexpressing IbbHLH66 enhanced drought tolerance, in sweet potato. IbbHLH118 directly binds to the E-boxes in the promoters of ABA-insensitive 5 (IbABI5), ABA-responsive element binding factor 2 (IbABF2) and tonoplast intrinsic protein 1 (IbTIP1) to suppress their transcription. IbbHLH118 forms homodimers with itself or heterodimers with IbbHLH66. Both of the IbbHLHs interact with the ABA receptor IbPYL8. ABA accumulates under drought stress, promoting the formation of the IbPYL8-IbbHLH66-IbbHLH118 complex. This complex interferes with IbbHLH118's repression of ABA-responsive genes, thereby activating ABA responses and enhancing drought tolerance. These findings shed light on the role of the IbPYL8-IbbHLH66-IbbHLH118 complex in the ABA-dependent drought response of sweet potato and identify candidate genes for developing elite crop varieties with enhanced drought tolerance.